[Bug-gmx_MMPBSA]: sander failed with prmtop COM.prmtop!

[dxf320]

Bug summary

CalcError:

/home/zhaoqin/miniconda3/envs/gmxMMPBSA/bin/sander failed with prmtop COM.prmtop!
I reduced the fillratio from 4 to 2,but can not solve the problem.

Terminal output

[INFO   ] Cleaning normal complex trajectories...
[INFO   ] Building AMBER topologies from GROMACS files... Done.

[INFO   ] Loading and checking parameter files for compatibility...
[INFO   ] Preparing trajectories for simulation...


[INFO   ] 10001 frames were processed by cpptraj for use in calculation.
[INFO   ] Starting calculations in 16 CPUs...
[WARNING] PB/RISM/NMODE will be calculated with multiple threads, make sure you have enough RAM.
[INFO   ] Running calculations on normal system...
[INFO   ] Beginning PB calculations with /home/zhaoqin/miniconda3/envs/gmxMMPBSA/bin/sander
[INFO   ]   calculating complex contribution...
              0%|          | 0/10001 [elapsed: 00:00 remaining: ?][ERROR  ] CalcError 

/home/zhaoqin/miniconda3/envs/gmxMMPBSA/bin/sander failed with prmtop COM.prmtop!
	
If you are using sander and PB calculation, check the *.mdout files to get the sander error


Check the gmx_MMPBSA.log file to report the problem.
  File "/home/zhaoqin/miniconda3/envs/gmxMMPBSA/bin/gmx_MMPBSA", line 8, in <module>
    sys.exit(gmxmmpbsa())
  File "/home/zhaoqin/miniconda3/envs/gmxMMPBSA/lib/python3.9/site-packages/GMXMMPBSA/app.py", line 101, in gmxmmpbsa
    app.run_mmpbsa()
  File "/home/zhaoqin/miniconda3/envs/gmxMMPBSA/lib/python3.9/site-packages/GMXMMPBSA/main.py", line 205, in run_mmpbsa
    self.calc_list.run(rank, self.stdout)
  File "/home/zhaoqin/miniconda3/envs/gmxMMPBSA/lib/python3.9/site-packages/GMXMMPBSA/calculation.py", line 142, in run
    calc.run(rank, stdout=stdout, stderr=stderr)
  File "/home/zhaoqin/miniconda3/envs/gmxMMPBSA/lib/python3.9/site-packages/GMXMMPBSA/calculation.py", line 625, in run
    GMXMMPBSA_ERROR('%s failed with prmtop %s!\n\t' % (self.program, self.prmtop) +
  File "/home/zhaoqin/miniconda3/envs/gmxMMPBSA/lib/python3.9/site-packages/GMXMMPBSA/exceptions.py", line 171, in __init__
    raise exc('\n\n' + msg + '\n\nCheck the gmx_MMPBSA.log file to report the problem.')
CalcError: 

/home/zhaoqin/miniconda3/envs/gmxMMPBSA/bin/sander failed with prmtop COM.prmtop!
	
If you are using sander and PB calculation, check the *.mdout files to get the sander error


Check the gmx_MMPBSA.log file to report the problem.
Error occurred on rank 9.
Exiting. All files have been retained.
Abort(1) on node 9 (rank 9 in comm 0): application called MPI_Abort(MPI_COMM_WORLD, 1) - process 9

gmx_MMPBSA.log

gmx_MMPBSA.log

Operating system

Ubuntu 20.04.6 LTS

gmx_MMPBSA Version

gmx_MMPBSA v1.6.3

Python version

3.12.4

Installation

None